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Structure paper

TitleHuman DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions.
Journal, issue, pagesJ. Am. Chem. Soc., Vol. 141, Page 8489-8502, Year 2019
Publish dateMar 27, 2018 (structure data deposition date)
AuthorsChang, Y.K. / Huang, Y.P. / Liu, X.X. / Ko, T.P. / Bessho, Y. / Kawano, Y. / Maestre-Reyna, M. / Wu, W.J. / Tsai, M.D.
External linksJ. Am. Chem. Soc. / PubMed:31067051
MethodsX-ray diffraction
Resolution1.6 - 2.15 Å
Structure data

PDB-5zlc:
Binary complex of human DNA Polymerase Mu with MndGTP
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-6aec:
Binary complex of human DNA Polymerase Mu with MnATP
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-6aeh:
Binary complex of human DNA Polymerase Mu with MnUTP
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-6ak5:
Binary Complex of Human DNA Polymerase Mu with MnGTP
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6ak6:
Binary Complex of Human DNA Polymerase Mu with MnCTP
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-6ak8:
Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Adenine and Incoming Ca-8oxodGTP
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-6ak9:
Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Cytosine and Incoming Ca-8oxodGTP
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-6akh:
Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Adenine and Incoming Mn-dUMPNPP
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-6ipd:
Post-catalytic Complex of Human DNA Polymerase Mu with Templating Adenine and Mn-8oxodGMP
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6ipe:
Post-catalytic Complex of Human DNA Polymerase Mu with Templating Adenine and Mg-8oxodGMP
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6ipf:
Post-catalytic Complex of Human DNA Polymerase Mu with Templating Cytosine and Mn-8oxodGMP
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-6ipg:
Post-catalytic Complex of Human DNA Polymerase Mu with Templating Cytosine and Mg-8oxodGMP
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-6iph:
Binary Complex of Human DNA Polymerase Mu with MndATP
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-6ipi:
Binary Complex of Human DNA Polymerase Mu with MndCTP
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-6ipj:
Binary Complex of Human DNA Polymerase Mu with MndTTP
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-6ipk:
Binary Complex of Human DNA Polymerase Mu with Mn8oxodGTP
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-6ipl:
Binary Complex of Human DNA Polymerase Mu with MgdATP
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-6ipm:
Binary Complex of Human DNA Polymerase Mu with MgdCTP
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-6ipn:
Binary Complex of Human DNA Polymerase Mu with MgdGTP
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATE / UTP*YM / Uridine triphosphate

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

ChemComp-CTP:
CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate

ChemComp-CA:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-8DG:
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM / HEPES

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-CL:
Unknown entry / Chloride

ChemComp-DUP:
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE

ChemComp-OXD:
OXALIC ACID / Oxalic acid

ChemComp-MG:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-PPV:
PYROPHOSPHATE / Pyrophosphate

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSFERASE / DNA polymerase / DNA break repair / TRANSFERASE-dNTP complex / DNA Polymerase Mu / Transferase-rNTP complex / TRANSFERASE/DNA / Transferase-DNA complex / 8-oxo-dGTP

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